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The Robot That Is Helping Unravel the Mystery of Ocean Microbes

Ocean microbes are key to global carbon and oxygen cycles, but they aren’t well studied due to challenges observing them at the right time and place. Now researchers have developed a new autonomous robot and sampling device that could help crack the microbial code.

Written by Paul Tullis Published on Read time Approx. 5 minutes
A long-range AUV cruises beneath the ocean surface during field trials in Hawaii.Image Courtesy of Elisha Wood-Charlson, University of Hawaii

For decades, scientists have used technology to study the behavior and interactions of cheetahs, baboons, lions and countless other terrestrial animals over time and distance. At sea, even for closely tracked species such as whales and sharks, these kinds of day-to-day life details, and how they may affect ecosystems, are much harder to monitor.

Now imagine how hard it is observing the tiniest ocean creatures – microbes – in their natural habitat. To date, nuanced observations of their changing roles in an ecosystem have been extremely limited. With new technology, that’s now changing.

About 80 miles (130km) north of Maui, Hawaii, a small fleet of robots has for the past few days been collecting samples of ocean microbes in an eddy about 70 miles (110km) wide, spinning counterclockwise in the North Pacific Ocean. This Thursday, the vehicles will be recovered and cracked open, their cartridges removed and the filters containing the samples taken out for later analysis, including whole genome sequencing.

“Looking at a day in the life of all these ocean microbes and tracking them to see what happens on a day-to-day basis is something that’s never been possible before,” said Edward DeLong, professor of oceanography at the University of Hawaii, Manoa, and coprincipal investigator on the project along with colleague David Karl.

Two long-range AUVs return from field testing offshore of Honolulu Harbor. (Image courtesy of Elisha Wood-Charlson, University of Hawaii)

Ocean microbes are notably understudied considering the crucial role they play for all life on the planet. They help produce at least half the oxygen in the atmosphere, and the amount of carbon they assimilate from it is equal to that of all terrestrial systems combined.

“If we’re interested in how much carbon dioxide is escaping from the Earth compared to how much is stored, these little guys are really on the front line for driving these processes,” said Mary Ann Moran, who specializes in bioinformatics and computational biology in the department of marine sciences at the University of Georgia.

Microscopic creatures also form the base of the marine food chain. And yet, said Pia Moisander, a marine microbiologist at the University of Massachusetts Dartmouth, “we don’t know what we don’t know” about ocean microbes. “Some really surprising discoveries are still coming out from marine microbial ecology, and a lot of that is made through technological development.”

The current expedition is the result of two converging technologies, both developed at the Monterey Bay Aquarium Research Institute (MBARI): long-range autonomous underwater vehicles (AUVs) and miniaturized environmental sample processors. The long-range AUVs have design features that save energy so they can travel for longer than typical underwater robots, including a specially designed propeller and components that reduce drag when diving or surfacing.

The environmental sample processors within the vehicles are small variations of devices MBARI has been building for the past decade or so. About the size of a 50-gallon (200-liter) drum, the earliest models were deployed on moorings on the seafloor to filter water and collect samples.

MBARI engineers Brett Hobson and Brian Kieft dunk-test an AUV in Honolulu Harbor. (Chris Preston © 2018 MBARI)

“There’s no technology out there like this, but the mooring has been a real detriment,” said Jim Birch, instrument group leader in the engineering department at MBARI. He and colleagues have spent years figuring out how to shrink the device to fit in a long-range AUV as a payload instrument. That involved devising cartridges to filter the seawater, putting several cartridges around a central ring. The long-range AUV moves one of 60 cartridges into place where it can open to the ocean and begin filtering water for up to 60 minutes.

Birch built the sampler to be smart enough so that it knows when a sufficient amount of biomass has been loaded onto the filter, triggering the cartridge to close. “Moving a liter of water through a very small filter in a very confined space was a big challenge,” he said. “For the first time, we can cover a lot of ground and bring these archived samples back.”

That’s important because of David Karl’s work at Station ALOHA, a site about 60 miles (100km) north of Oahu where he and colleagues have been taking biological and other measurements for 25 years. He has shown that “a major fraction of the biological activity for a whole year can take place in a few days or a week,” Moran said. “Those episodes are really important for the carbon budget [in climate models], but if you’re not at the right place at the right time you’re not able to get it.” Research vessels need to be booked up to a year in advance and cost thousands of dollars per day to operate. AUVs are comparatively cheap and can be deployed quickly in response to events observed by satellite.

North of Maui, while one long-range AUV is taking samples, another “flies” in circles around it, ascending and descending at heights of 165–820ft (50–250m) to take measurements of temperature, conductivity and other conditions. Meanwhile, a Wave Glider, a seafaring robot on the surface, relays communications between scientists on land and a ship and the long-range AUVs.

Engineers Brett Hobson from MBARI and Gabe Foreman from the University of Hawaii prepare a long-range AUV for field trials. (Chris Preston © 2018 MBARI)

“You stop your Netflix movie and go, ‘Let me check on the vehicle,’ and set it to a different waypoint on [your] phone, and off it’ll go,” said Birch.

Ocean eddies, such as the one the robot fleet is now sampling, are important for moving heat and nutrients up and down the water column, and microbes tend to get stuck in them. They’re like isolated cities of microbial populations, each photosynthesizing and respirating. The long-range AUVs, which can travel around 600 miles (1,000km), will help track and survey them.

Back at the lab, the team’s scientists will be able to see which genes are expressed at what time of day, how the population varies in space and changes over time and the dynamics between different species. “This project gives higher resolution than we’ve ever had before,” DeLong said. “We’re taking snapshots of the microbial community and once we get the genomic information, the stills can be put together to form a movie.”

Now that DeLong and Karl have received the equipment from MBARI, they’re going to be the envy of marine microbiologists the world over. “I’d love to get my hands on these types of instruments,” Moisander said. “This is definitely where the field needs to go, so it’s super-exciting they’re doing this work.”

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